Applying Spatial Transcriptomics to the Human Heart: A Practical Guide for Translational Studies

Spatial transcriptomics and single-cell methods are changing the questions we can ask about the human cardiovascular system. In this review, we share lessons learned from applying spatial profiling to human cardiovascular samples. We walk through experimental considerations, sampling, fixation, and ribonucleic acid quality control, then compare sequencing-based and imaging-based platforms within a 2-stage "discovery then validation" framework. We propose a heart-aware analytical pipeline: spatially informed quality control, normalization respecting the outsized transcriptome of cardiomyocytes, thoughtful segmentation, and honest assessment of reproducibility. We consider how spatial data can be woven together with single-cell, epigenomic, and proteomic layers, and look ahead to emerging frontiers including integration with cardiac imaging foundation models. Our hope is that spatially resolved molecular data will reveal new tissue niches to target for precision cardiovascular therapies.